Did you read the error message? It says: Variable 2 has character string Female Variables should be continuous numbers You have listed Gender and Race as strings, they have to be numbers (eg, 1, 2) You probably want to have these be discrete variables instead of continuous
On 11/10/2021 6:20 PM, Zeng, Qi wrote:
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Hi Douglas,
Here is the command line: mri_glmfit \ --y rh.thickness-rate.MyStudy.10.mgh \ --fsgd FSGD/MyStudy.fsgd dods\ --C Contrasts/Case-Control_age_gender_race_etiv.mtx\ --surf fsaverage rh \ --cortex \ --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \ --eres-save
Also error message in terminal: gdfRead(): reading FSGD/MyStudy.fsgd WARNING: variable 1 is "Gender" which is often a discrete factor The proper way to handle discrete factors is to create classes. See *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples https://secure-web.cisco.com/1NHVxBIRnha6EjEdEho81-VE9d-vjJ6ivzt10z28vhX9c94pCwosQpkLG4Hfu3nLYp7KMDne5wAk9mK45YIQJEZBe6UlteF2wwLohmZJzp070UjHvv6fqugRAkgBk0uNO3Fsgo5BzblW95J5iO5sXWwZLK-LGAZJJTBaU7mLTkO5L70JRSscCW3pdc-G5KchZMbVyeY65gGH4w5MMIYBSVHvX03spMjZ85XkHbkgYYmWXTFnzqUGhqGgHygP5sLeR7OWPKIzEb7X3pHi7POf0UyEHJAZpQLU9bgT2BnOcClt0kW4mll1ODQDC2Y0U7-0f/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base Variable 2 has character string Female Variables should be continuous numbers FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input
Also attached FSGD file below. Thank you so much for the help!
Best, Zeng
On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
please send your command line and full terminal output as well as the fsgd file On 11/10/2021 5:12 PM, Zeng, Qi wrote:External Email - Use Caution Hi Freesurfer experts, Here, I want to design a simple group comparison (two levels: Case vs. Control) and also count for 4 covariates (two continuous and two categoricals). However, the GLM model cannot recognize my discrete variables. What do you suggest to change? >> FSDG file: GroupDescriptorFile 1 Title MyStudy Class Control Class Case Variables agegenderrace eTIV Inputsub001_baseControl85FemaleWhite1350519 Contrast: >> Design matrix for Case-Control and regress out the effect of age, gender, race, and eTIV. -1 1 0 0 0 0 0 0 0 0 Best, Zeng _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/12U-W_RSiRIJWjQDCBYfqvGXFwFXZQgpm04lVl3v5K0t8IYtpEx5cD1xcltIygwIKmo05cI6l-2nfk9uxFgBdWGoedjfSO3t3_Hbh1NQQDj4gxzchE8QF5shV5fOP8ukCqp6pHmkq140ase4PWm8-1key4YN4H_tSk9Wh09gbrQK4nERYcXWQYw8fkpCXcQ3U5MXxTyPgoKWJY68te_B_XbFVhWWhzaz65RTcy1JyJlfZLY6Nyv0LACWWHmWU4NzLmBeHSMh8lssnATJq77P16Tl72f8QkK6_lB_cDhEWqJocd9RxUL3qeDAwtK9UbRCY/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/12U-W_RSiRIJWjQDCBYfqvGXFwFXZQgpm04lVl3v5K0t8IYtpEx5cD1xcltIygwIKmo05cI6l-2nfk9uxFgBdWGoedjfSO3t3_Hbh1NQQDj4gxzchE8QF5shV5fOP8ukCqp6pHmkq140ase4PWm8-1key4YN4H_tSk9Wh09gbrQK4nERYcXWQYw8fkpCXcQ3U5MXxTyPgoKWJY68te_B_XbFVhWWhzaz65RTcy1JyJlfZLY6Nyv0LACWWHmWU4NzLmBeHSMh8lssnATJq77P16Tl72f8QkK6_lB_cDhEWqJocd9RxUL3qeDAwtK9UbRCY/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1YGeBpazeZXSLfsCEO4_vE11nUNbtdYgN2Tpx1anls1heh4xx3r9SAPXdptyAb3NQFEWW_wDyFNgmJO__d_VUJ4ZoDc6uOlHryomgspKnDLXlJUxYcwmHguKWwgYZamww28y60Aeq0gJLeaCWbwoahgMRrH8-z5ta2ABmTVYMWcGgKuwlAOzE5hf9artWSY3R9z36qyZBlqSphIF6fAWzYMk0dO_RcNVOZUxOpurwkn6dbDtArOd-sJXNda8_EWB9OYHZ2g5P_tcrpodvlf-MKZGF3VZ3bJH8C4OO5j6Di85pQ4alax7KCxKTYsi_o7YJ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
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